The Twelfth Doctor's new Adventure
by VHAL9000
Summary: (Takes place after the events of Halo 4 and the "Time of the Doctor" ) After the Cortana had "died", her chip gets send to another universe, where the Twevelth Doctor picks it up, after regenerating on Trenzelore. Using his sonic screwdriver and the power of the TARDIS, the Doctor brings Cortana back to life. What will happen next?


_**Chapter 1: The Twelfth Hour, the fall of the Eleventh**_

The Eleventh Doctor saved everyone at the battle of Trenzelore. The planet was supposed to be his final resting place, his tomb. But fortunately luck turned in his favor. With encouragement from Clara Oswald, the Time Lords appeared from the time crack, and gave the Doctor a new set of regenerations. The Doctor impressively used his regeneration energy to defeat the Daleks singlehandedly. After the trouble was over, Clara searched for the Doctor and saw he was young again.

"_Doctor you're young again."_

"_This is just the reset. A whole new regeneration cycle.. Taking a bit longer.." _

"_We all change all throughout our lives. But that's good we gotta move forward, so long as we remember the people that we used to be."_

"_I won't remember this moment. Not one day. I swear. I will always remember when the Doctor was me." _

"_Please don't change." _

After Clara pleaded the Doctor not to regenerate, the Doctor smiled at her and regenerated in a flash jerking his head to the side. A golden shine changed his appearance from young to old.

"Kidneys! I got new kidneys!" The newly regenerated Doctor exclaimed as he felt a surge of pain hit him. "I don't like the color."

"What is the color of your kidneys?" Clara asked.

Then the Tardis began to shake.

"What's happening?" Clara panicked.

"We appear to be crashing."

"What?" Clara asked.

"Stay calm." The Doctor replied, as he was trying to tinker with the controls. "Just one question."

Clara looked at him quickly.

"Do you happen to know how to fly this thing?" The Doctor asked, as the Tardis began to shake, until it suddenly crashed, knocking both the Doctor and Clara out.

_**Chapter 2: Finding Cortana's chip**_

"Doctor! Doctor! Wake up" Clara shouted as she pushed the Doctor to wake him up.

The Doctor woke up slowly, but shook his head in pain.

"What happened?" The Time lord asked.

"We seemed to have crashed." Clara replied.

"How long were we knocked out?" the Doctor asked.

"I dunno." Clara said as she shook her head.

"What about the Tardis?" 13 asked.

"It seems to be okay." Clara said as she observed the blue box, whose bottom seemed to be buried underground. However, the doors and the top were visible enough for the two to get in.

The Doctor got up slowly, but something rectangular caught his eye. He picked it up slowly, and pressed on its button. Nothing happened.

The Doctor took out his sonic screwdriver and scanned the Rectangular device.

"What is it, Doctor?" Clara asked.

"It seems to be a device that belonged to an AI." He replied.

"AI?"

"Artificial intelligence." The Doctor replied.

"You mean like the Cybermen?" Clara asked.

"Not really." The Doctor said, as he put the rectangular chip in his pocket. "Artificial Intelligence means something made has developed a living brain. The Cybermen are in actuality are humans combined with cybernetics."

"An artificial intelligence is more like a robot, and cybermen are not robots." Twelve said, as he got into the Tardis.

Clara curiously followed him inside.

"What are you doing, Doctor?" Clara asked as she saw him put the chip in the Tardis.

"This chip has a familiar shape that fits in one of the Tardis slots. Perhaps she can analyze it, and tell us what we need to know." The Doctor replied, and Clara nodded slightly.

Then in a quick flash, a hologram appeared and stood on the Tardis controls. She was blue, transparent, and apparently naked. Her hair was short cut, and her eyes were clear as the blue skies above.

"Chief, I'm picking some readings." She said, and then she suddenly looked at the Doctor. "You're not the Chief."

"Who's that?" The Doctor asked.

"He's my friend, and my companion. My equal." Cortana replied.

"What's your name?" Clara asked.

"My name is UNSC Artificial Intelligence serial number: CTN 0452-9 Cortana. I was an AI aboard the Infinity, and I'm a companion to Master Chief." Cortana explained.

"UNSC? As in United Nations Space Command?" The Doctor asked.

"Yes." Cortana replied. She concentrated on the Doctor. "How did you know?"

"I encountered them on two occasions." The Doctor replied.

"But I have looked through all the databases aboard the Infinity, I haven't seen any human like you before." Cortana protested.

"Who said I was human?" The Doctor asked, and Cortana was baffled by this.

"What are you?" Cortana replied. She performed a quick scan on his body. "Two hearts?" Cortana asked.

The Doctor nodded.

"But you're not a Covenant Alien.." She said

"That's correct. I'm not, But I'm something else." The Time lord replied.

"What?" Cortana asked.

"I'm a Time Lord" The Doctor spoke silently, and Cortana was shocked and surprised.

**Chapter 3: John's sadness and determination**

After defeating the forerunners and saving the world, John 117 watched as his armor was slowly removed from his body. Although the battle was won in his favor, he did have to make one of the biggest sacrifice of all: Cortana, his trustworthy AI. She was everything to him, his past, his present, possibly his future. She stood by him in the darkest of times, helping him to fight the deadly Covenant race. Now the thought of her death broke the tough barriers of his psyche. But he was becoming more of a human and less of a machine.

_Which of us is the machine, you or me? _

John pondered this question, and finally came to the realization that the machine was him all along. He was more stoic towards the other Spartans, and he had no social life.

Adjusting to life without Cortana will be hard and tough. But something told him, that she was still alive, and it was up to him to save her, whatever the cost.

**Chapter 4: Returning Cortana to John **

"So she's a time machine?" Cortana asked, as she observed the interior of the Tardis.

"Yep. It's my Tardis. Time and Relative Dimension in Space." The Doctor replied.

"Well I must admit, she's a wonderful machine." Cortana commented.

"Yes she is." The Doctor spoke agreegingly.

"So you're a timelord right? Isn't that race extinct?" Cortana asked, and the Doctor froze.

"How do you know that?" He asked her.

"I just read through some records, and I saw that the Time Lords were once powerful people, but then one Time Lord, caused their extinction, and not only that but the extinction of another race called the Daleks." Cortana replied.

"They're not dead." The Doctor spoke silently. "They're in a time lock."

"Time lock?" Cortana asked.

"Nevermind." The Doctor spoke. "Now the more pressing matter at hand is to get you back to your world."

**Chapter 5: Meeting the Chief**

As Master Chief contemplated on how to get Cortana, a blue box mysteriously materialized in the ship.

"What the heck is that?" John 117 spoke, as he got up.

Suddenly Spartan troops arrived and surrounded the box. They aimed their guns at it attempting to shoot it.

"Put your hands up in the air quietly and get out of the box! We don't want to use lethal force!" A Spartan spoke.

Then the Doctor and Clara raised their arms as they got out of the Tardis.

"We don't mean any trouble, we're just here to deliver a gift." The Doctor spoke.

"To whom?" The Spartan asked as he still pointed the gun at the two.

"I have a gift for Master Chief, aka Sierra 117." The Doctor spoke, as he revealed Cortana's chip.

Master Chief's eyes widened as he saw the chip. He went over to the Doctor and snatched the chip.

"So this is what you look like, Master Chief." The Doctor said looking at his face.

"Call me John." John replied, as he held the chip in his hand.

"Your AI, Cortana, she's in that chip." The Doctor said.

"I know that. But what did you do to her?" John asked with an angry tone to the Doctor.

"I only repaired her. She seemed to be not working when I first pressed the chip." The Doctor spoke, but John was still skeptical of him.

"If you don't believe me, try it yourself." The Doctor said, and John looked at him for a moment.

He pressed the button on Cortana's chip, which revealed his former companion.

"Hello John." Cortana said, and John was a bit startled.

"Cortana." John said. "You died. How?"

"I came back to life." Cortana replied. "The Doctor repaired me."

"The Doctor?" John said, and he looked at the man that was staring at him.

"Thank you." John spoke to the Doctor, who nodded his head.

"If there's no trouble, can I speak to you alone?" John asked, and the Doctor nodded his head.

The Spartans who surrounded them walked away to do their regular jobs on the ship.

Then John and the Doctor walked away to a separate room. Before they entered the room, a Spartan came to John.

"Should we trust him, Sir?" The Spartan asked.

"He fixed Cortana. I think he's trustworthy." John 117 replied as he entered the room with the old 12th doctor.

**Chapter 6: Deciding to save Halsey**

"Tell me how you fixed Cortana." John asked.

"It's kind of a long story." The Doctor replied.

"I can handle anything. Shoot." John spoke.

"Ok. So when I first found your digital friend, I used my sonic screwdriver to analyze it. Then I took it back to the TARDIS, and inserted the chip in her mainframe." The Doctor explained.

"Your?" John asked.

"Time and Relative Dimension in Space." Cortana interrupted. "He has a time machine, John."

"But why do you refer a time machine as 'she'?" John asked.

"The TARDIS is sentient, and is female. Am I correct, Doctor?" Cortana asked, and the Doctor nodded his head again.

"Ok, this day gets weirder and weirder." John said as he shook his head. "First you die, then you come back with an old man in a blue box that supposedly travels through time."

"There is a possibility, John. Anything can happen." Cortana said,

"I see." John said.

Meanwhile, Clara was with a group of male Spartans who were harassing her.

"So why are with you with an old man in a blue box?" A Spartan asked.

"Is he your grandfather or something?" Another asked.

"No." Clara said. "He's just a friend."

Then Palmer came.

"Can you quit asking her so many questions? The girl needs a break. Give to her."

"Ok, Mother." A Spartan replied, and the Palmer aimed her rifle at him.

"Ok. Ok." The Male Spartan spoke. "I'm sorry." Palmer lowered her rifle.

Meanwhile, the Doctor and John had finished talking.

"I better be going." The Doctor said as he got up.

"No, you should stay." John replied, and the Doctor looked at him funny.

"Hm." The Doctor said. "I guess Clara and I could stay here for a while."

Then he looked at Cortana. "Who's your creator?"

Cortana and John looked at each other.

"My creator is Dr. Catherine Halsey." She replied.

"Catherine Halsey?" the Doctor asked. "You mean the one that created the Spartan Program?"

"You know her?" John asked.

"I have heard of her before. Brilliant women she is. Extraordinary." The Doctor replied.

"And I also heard that that Parasite Flood was destroyed." The doctor said. "Is it true?"

Cortana and John both nodded.

"Nasty creature he was. Eating away of the minds and bodies of others, for survival, is just disgusting and repulsive." The Doctor said.

"How do you know all of this?" Cortana asked.

"I was sort of there during the Human- Covenant- Flood war. I sort of hid during the war." The Doctor replied.

"By the way, where is Dr. Halsey?" The Doctor asked. "Is she here on this ship?"

John froze. "She was arrested and she escaped."

"Do you know where she is?" The Doctor asked.

Cortana and John both shook their heads.

"I guess we found our new objective." The Doctor spoke as he grinned a little.

**Chapter 7: The Search begins**

The Doctor, John, and Clara walked towards the TARDIS, when they were stopped by Captain Lasky.

"Just where do you think you're going?" He asked.

"We're going to find Dr. Halsey." John said, as he was in his Green Spartan Armor.

The Captain shook his head. "I'm afraid I cannot let you three leave this ship."

"With all do respect sir; we need to get her back from the Covenant." John replied.

"I'm sorry, John. I know how much she meant to you, but Dr. Halsey is now an enemy of the UNSC. An issue was given by higher powers to execute her for her crimes" Lasky replied.

"What crimes?" The Doctor asked.

"Well for one thing she kidnapped innocent children and bred them into mindless killing machines." Lasky explained.

"She did that to make us stronger against the Covenant." John retorted angrily.

"The other crimes?" The Doctor asked

"She is also charged with aiding the enemy." Lasky stated.

"You have no proof." John defended.

"Yes, he does, Chief." Palmer said. "We saw her communicated with the enemy through her electronic device."

The Chief turned to Lasky.

"With all do respect, Sir. I'm going to search for Halsey whether you like it or not."

The Captain sighed. He didn't like Chief disobeying orders, but he didn't want to shoot him either.

"Fine." He said. "Just be careful, Chief."

With a nod, the Chief walked into the Tardis, along with Clara and the Twelfth Doctor.

Chapter 8: The Time lord vs the Sangheili

Jul' Mdama walked from side to side figuring out how to get revenge at humanity. They beat the Covenant thousands of times, and Mdama wanted payback. Their kind sickened him.

"_**Have you come up with a plan to get back at Humanity, Halsey?" **_He spoke in the ancient Sanghelios language.

"Not yet. I need more time." Halsey replied. "Revenge such at this must be met with the sufficient amount of time."

Suddenly, a blue box materialized from nowhere surprising both Halsey as well as Mdama.

"**How did that blue box come here**?" Mdama asked.

"I don't know. Did it use any type of Forerunner Technology?" Halsey asked.

Then the box opened. Out of the box, appeared Master Chief, Cortana, Clara and Doctor.

The Doctor looked at Mdama and smirked.

"**So we finally meet Jul' Mdama, of Sangehelios. Or should I call you, 'Didact's hand'?"** The Doctor asked in Sanghelios.

The Sangheili shipmaster growled at the Doctor for speaking ill of him.

"**How dare you speak of me, human**! " Mdama retorted. **"I shall crush you painfully."**

"**Fear me, Mdama. I'm no ordinary human. I'm not a human at all. I'm a time lord. The deadliest time lord you'll ever meet. I'm the oncoming storm, the beast, and your doom**." The Doctor replied.

Mdama realizing who the Doctor was, backed away. **"You have some nerve to come here, Beast. But what can you do? What are you here for?" **

"Oh I can do lots." The Doctor replied this time in English. "For example, I can turn off your ship's systems and defenses." He pulled out his sonic screwdriver.

"**What is that device? Some type of forerunner technology?"** Mdama inquired.

"It's a Sonic screwdriver. Doesn't kill, doesn't wound, doesn't maim. But one thing is does do: turns off a Ship's defenses." He quickly pressed on the screwdriver which turned the Ship's power grid off.

Suddenly the ship began to move off course, and it was shaking at the exact same time.

"Everyone to the Tardis!" The Doctor shouted, as everyone except Mdama got in the Blue box.

"**I will get you, Beast. I will kill you and feast upon your bones! Your death shall be my ascension!"** Mdama growled, as he was pushed back to the end of the ship.

"Not going to happen, Sangheili." The Doctor replied, as he shut the Tardis's doors. The Tardis started to dematerialize, disappearing from all view.

**Chapter 9: Nowhere to go **

The Tardis floated in all of time and space. A tiny blue box in a sea of black.

"What are we going to do?" Clara asked.

"We need to go back to the UNSC." John spoke.

"I don't think that will work, John." The Doctor replied. "The UNSC wants Dr. Halsey dead, so consider that she is alive. They'll try to kill you, because they'll think you're now an enemy for helping her."

"He's right, John." Dr. Halsey. "We can never go back."

"So they'll come and attack all of us?" Clara spoke.

"If they see us." Cortana piped in. "And I know I said this once already, but this box is amazing. She can travel through time and space at any time. It's incredible."

Dr. Halsey smiled for a bit, but then looked at the Time lord who was manning the control.

"So your name is the Doctor?" Halsey asked.

"Yes." The Doctor replied.

"But that's a title."

"I know."

"So you're saying that your name is 'the Doctor'?" Dr. Halsey inquired.

"Yes, and I am also a Doctor too. " The Doctor said.

"And your sonic screwdriver." Dr. Halsey spoke. "Are you sure it isn't Forerunner based."

"Nope." The Doctor replied. "It's Gallifreyan. I made it on my own."

"Gallifreyan?" Halsey asked.

"Have you heard of the planet Gallifrey?" The Doctor asked.

"I have heard only a little bit." Halsey replied.

"Well I'm going to tell you a story." The Doctor said.

**Chapter 10: The Doctor's tale**

"Long time ago, before the Covenant, before the Forerunners, before Humanity, there lived a race called the Time Lords. They lived on the planet, Gallifrey, which was in the constellation of Kasterborus. Gallifrey was a beautiful planet. It had children who frolic on the warm fields every day, and our education was different to that of Earth. It was beautiful. Absolutely beautiful. But then one day changed it all. The Time War." The Doctor explained.

"Time War?" John asked, and the Doctor nodded.

"The Time War was a war between the Time Lords and the Daleks. Am I correct?" Cortana asked.

"Yes." The Doctor responded. "The Time War was between us Time lords, and a race called the Daleks. They were most ferocious of all the species in the universe and they are not to be trifled."

"Go on." Dr. Halsey spoke, as she was interested in the Time Lord's tale.

"So, in this war, there was one man who didn't want to both sides to kill each other. In other words, he didn't want the fighting to continue. So he destroyed the Time lords, and the Daleks in order to end the war." The Doctor sadly explicated. "Gallifrey burned, with the end of the Time Lords."

"But you said earlier that the Time Lords survived." Cortana spoke.,

"I was getting to that." The Doctor spoke. "So after the war, the Time Lords apparently survived and tried to take over Earth. Fortunately, I stopped them, and send them back in a time lock to the days of the war. They are now in a parallel pocket universe along with Gallifrey"

"But what about the daleks?" John asked.

"I don't much about the Daleks, but I do remember destroying their ship, at Trenzelore. There may be more in the universe." The Doctor said.

"And who is that man you spoke of?" Dr. Halsey asked

"Me." The Doctor replied. "I'm the Daleks's worst enemy, and their greatest foe. **I am a monument to all their sins**."

**Chapter 11 : Friendships form**

On the UNSC ship, Captain Lasky and the crewmembers were debating on the whereabouts of Dr. Halsey.

"Do you think the Chief is going to kill Halsey, sir?" Palmer asked.

"I highly doubt that. Master Chief cares more about her than any of us." Lasky replied.

"What if they both come back here?" She asked.

Lasky shook his head. "That's up to higher command to make the decision whether to kill them or let them stay. But mostly likely, they would want both of them dead, as scary as it sounds."

"But I don't want to go against the Chief." Palmer said.

"I don't either, but as soldiers we need to obey orders." The Captain answered.

Back on the Tardis, Dr. Halsey and the Doctor were playing a game of chess.

"Impressive moves, Doctor." Halsey commented. "How did you get to play this good at chess?"

"The Time Lords invented chess, my dear Catherine." Twelve replied with a smile.

While the two Doctors played chess, Clara looked at Master Chief, who was staring at the Tardis's wall.

"What are you thinking about?" Clara asked, and Master Chief turned around.

"Mind if I join you?" She asked.

"No." The Chief replied, and Clara stood by him.

"Do you ever once look at space and wonder how many stars there are?" Clara asked.

The Chief stood silent, stoic as ever.

"I guess you don't know either." Clara replied with a kind smile. "I don't know the answer either. I'm just a school teacher. But the Doctor knows."

The Chief looked at the Doctor. "Why do you travel with him? What makes him special?"

"I dunno. I think it's just because he's fun to be around. He's funny, smart, and adventurous. He's also good hearted, and does his best to save the universe from danger." Clara said.

"So this Doctor is a very important person?" the Spartan asked, and Clara nodded.

"He's so important, that I laid my life down to save his." Clara smiled. "That's why I'm called the 'Impossible Girl'. "

"I see." The Chief said,

**Chapter 12: Ending?**

Back at the UNSC ship, Captain Lasky got a call from higher powers.

"Yes, sir. It shall be done." He said, as he put down the phone.

"What is it, sir?" Palmer asked. "What did they say?"

"They gave the order." He replied, as his face was distorted with sadness and grief.

"The order?" She asked.

"They want us to kill Doctor Hasley." He said

"I know that." She replied.

"But." He said.

"But?" She asked.

"They want us to kill the Chief as well." He muttered, and Palmer was shaken by his statement. How could she go against the man who saved Humanity thrice from the Covenant, the Flood, and the Forerunners. How could she go against her hero?

"I can't." She choked.

"I'm sorry, Palmer. It must be done." He spoke silently, as he looked away.


End file.
